NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
O93937 UniProt NPD GO	PYR1_EMENI	Protein pyrABCN [Includes: Glutamine-dependent carbamoyl-phosphate (EC 6.3.5.5); Aspartate carbamoyl ...	0.13	-	nuc	0					2275
Q10358 UniProt NPD GO	RER1_SCHPO	Protein rer1 (Retention of ER proteins 1)	0.13	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				184
Q9GP71 UniProt NPD GO	YELL_DROMD	Protein yellow precursor	0.13	-	mit	1 *	Secreted protein				568
P08587 UniProt NPD GO	TGM2_CAVCU	Protein-glutamine gamma-glutamyltransferase 2 (EC 2.3.2.13) (Tissue transglutaminase) (TGase C) (TGC ...	0.13	-	mit	0					689
P21981 UniProt NPD GO	TGM2_MOUSE	Protein-glutamine gamma-glutamyltransferase 2 (EC 2.3.2.13) (Tissue transglutaminase) (TGase C) (TGC ...	0.13	-	mit	0		cytosol [TAS] extracellular matrix (sensu Metazoa) [TAS] membrane [TAS]			686
Q8WUK0 UniProt NPD GO	PTPM1_HUMAN	Protein-tyrosine phosphatase mitochondrial 1, mitochondrial precursor (EC 3.1.3.48) (EC 3.1.3.16) (P ...	0.13	-	cyt	0	Mitochondrion; mitochondrial inner membrane (By similarity). Associated with the inner membrane (By ...		609538		201
P30558 UniProt NPD GO	PAR1_MOUSE	Proteinase-activated receptor 1 precursor (PAR-1) (Thrombin receptor)	0.13	-	end	7	Membrane; multi-pass membrane protein				430
P17553 UniProt NPD GO	WNT3_MOUSE	Proto-oncogene protein Wnt-3 precursor	0.13	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix				355
P27446 UniProt NPD GO	FYN_XIPHE	Proto-oncogene tyrosine-protein kinase FYN (EC 2.7.10.2) (P59-FYN)	0.13	-	nuc	0					536
Q9Y5F1 UniProt NPD GO	PCDBC_HUMAN	Protocadherin beta 12 precursor (PCDH-beta12)	0.13	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606338		795
P35247 UniProt NPD GO	SFTPD_HUMAN	Pulmonary surfactant-associated protein D precursor (SP-D) (PSP-D)	0.13	-	exc	0	Secreted protein; extracellular space	endocytic vesicle [TAS] extracellular region [TAS] lysosome [TAS]	178635	1PWB	375
Q8T635 UniProt NPD GO	CU20_MANSE	Pupal cuticle protein 20 precursor (MsCP20) (MS-PCP20)	0.13	-	vac	0	Synthesized in the epidermis during the larval-pupal transformation and then secreted into the phara ...				200
Q8MUC5 UniProt NPD GO	CU36_MANSE	Pupal cuticle protein 36 precursor (MsCP36) (MS-PCP36)	0.13	-	mit	0	Synthesized in the epidermis during the larval-pupal transformation and then secreted into the phara ...				342
Q24998 UniProt NPD GO	CUP52_GALME	Pupal cuticle protein PCP52 precursor (GMPCP52)	0.13	-	exc	0					353
Q9C8F7 UniProt NPD GO	RL301_ARATH	Putative 60S ribosomal protein L30-1	0.13	-	nuc	0					112
Q11180 UniProt NPD GO	YPC3_CAEEL	Putative ABC transporter C05D10.3 in chromosome III	0.13	-	end	5	Membrane; multi-pass membrane protein (Potential)				598
P23128 UniProt NPD GO	ME31_DROME	Putative ATP-dependent RNA helicase me31b (EC 3.6.1.-) (Maternal expression at 31B)	0.13	-	nuc	0					459
Q9H4K7 UniProt NPD GO	GTPB5_HUMAN	Putative GTP-binding protein 5	0.13	-	mit	0					406
Q9LUL6 UniProt NPD GO	ATL3E_ARATH	Putative RING-H2 finger protein ATL3E	0.13	-	cyt	1 *					204
Q27504 UniProt NPD GO	CAH3_CAEEL	Putative carbonic anhydrase 3 (EC 4.2.1.1) (Carbonate dehydratase 3)	0.13	-	cyt	0					246
P46560 UniProt NPD GO	KICB3_CAEEL	Putative choline kinase B3 (EC 2.7.1.32)	0.13	-	cyt	0					314
P34340 UniProt NPD GO	COL90_CAEEL	Putative cuticle collagen 90	0.13	-	exc	1 *					305
P34391 UniProt NPD GO	COL91_CAEEL	Putative cuticle collagen 91	0.13	-	nuc	1 *					278
Q27517 UniProt NPD GO	C13A3_CAEEL	Putative cytochrome P450 CYP13A3 (EC 1.14.-.-)	0.13	-	end	2 *					520
Q27514 UniProt NPD GO	C13A5_CAEEL	Putative cytochrome P450 CYP13A5 (EC 1.14.-.-)	0.13	-	nuc	1 *					520
Q09850 UniProt NPD GO	ENG2_SCHPO	Putative endo-1,3(4)-beta-glucanase 2 (EC 3.2.1.6) (Endo-1,4-beta-glucanase 2) (Endo-1,3-beta-glucan ...	0.13	-	nuc	0	Membrane; multi-pass membrane protein (Potential)				706
Q10205 UniProt NPD GO	RRP43_SCHPO	Putative exosome complex exonuclease RRP43 (EC 3.1.13.-) (Ribosomal RNA-processing protein 43)	0.13	-	pox	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)				270
Q9URX4 UniProt NPD GO	YFZB_SCHPO	Putative family 31 glucosidase C1039.11c precursor (EC 3.2.1.-)	0.13	-	exc	0	Spore rim				995
Q10499 UniProt NPD GO	YDGE_SCHPO	Putative flavoprotein C26F1.14C	0.13	-	mit	0					575
Q94CD8 UniProt NPD GO	E134_ARATH	Putative glucan endo-1,3-beta-glucosidase 4 precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolas ...	0.13	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor				505
Q10427 UniProt NPD GO	YQ29_SCHPO	Putative glycosyl hydrolase C11E10.09c (EC 3.2.1.-)	0.13	-	mit	0					478
P34302 UniProt NPD GO	YKQ7_CAEEL	Putative glycosyl transferase C06E1.7 in chromosome III (EC 2.-.-.-)	0.13	-	mit	1 *					365
Q9CA75 UniProt NPD GO	GT5_ARATH	Putative glycosyltransferase 5 (EC 2.4.-.-) (AtGT5)	0.13	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				457
Q4HWQ2 UniProt NPD GO	CCPR2_GIBZE	Putative heme-binding peroxidase (EC 1.11.1.-)	0.13	-	cyt	0					331
Q9FM66 UniProt NPD GO	PEL21_ARATH	Putative pectate lyase 21 precursor (EC 4.2.2.2)	0.13	-	vac	0					392
Q9SZG4 UniProt NPD GO	PSK4_ARATH	Putative phytosulfokines 4 precursor (AtPSK4) [Contains: Phytosulfokine-alpha-like (PSK-alpha-like) ...	0.13	-	exc	0	Secreted protein (By similarity)				87
P34610 UniProt NPD GO	PCP1_CAEEL	Putative serine protease pcp-1 precursor (EC 3.4.-.-)	0.13	-	end	0					565
Q21751 UniProt NPD GO	EAA6_CAEEL	Putative sodium-dependent excitatory amino acid transporter glt-6	0.13	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				558
P25616 UniProt NPD GO	YCQ5_YEAST	Putative uncharacterized protein YCR015C	0.13	-	nuc	0					317
O43023 UniProt NPD GO	YGV9_SCHPO	Putative zinc metalloprotease C354.09c in chromosome II	0.13	-	mit	1					794
P52902 UniProt NPD GO	ODPA_PEA	Pyruvate dehydrogenase E1 component alpha subunit, mitochondrial precursor (EC 1.2.4.1) (PDHE1-A)	0.13	-	mit	0	Mitochondrion; mitochondrial matrix				397
Q06437 UniProt NPD GO	ODPAT_RAT	Pyruvate dehydrogenase E1 component alpha subunit, testis-specific form, mitochondrial precursor (EC ...	0.13	-	mit	0					391
P34150 UniProt NPD GO	RACD_DICDI	RAS-related protein racD	0.13	-	nuc	0					254
Q9GPS3 UniProt NPD GO	RACF2_DICDI	RAS-related protein racF2	0.13	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				193
Q9FYF7 UniProt NPD GO	Y1736_ARATH	REF/SRPP-like protein At1g67360	0.13	-	cyt	0					240
Q9LM69 UniProt NPD GO	ATL1B_ARATH	RING-H2 finger protein ATL1B	0.13	-	nuc	1 *					197
Q8QG64 UniProt NPD GO	RBX1_SALSA	RING-box protein 1 (Rbx1) (Hyperosmotic protein 21)	0.13	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				108
Q9JJT0 UniProt NPD GO	RCL1_MOUSE	RNA 3'-terminal phosphate cyclase-like protein	0.13	-	mit	0	Nucleus; nucleolus (By similarity)	nucleolus [IDA]			373
O43347 UniProt NPD GO	MSI1H_HUMAN	RNA-binding protein Musashi homolog 1 (Musashi-1)	0.13	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)		603328		362
Q9Y3V2 UniProt NPD GO	RWDD3_HUMAN	RWD domain-containing protein 3	0.13	-	cyt	0					195

You are viewing entries 60301 to 60350 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.